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Function

Write a list file of the logical OR of two sets of sequences

Description

listor reads in two sets of sequences (typically specified as list files) and writes out a list file that result from the logical union of the two sets. A list file is a file with a list of Uniform Sequence Addresses (USAs), for example, a list of file names. When comparing sequences from the input sets, no use is made of the ID name or accession number; only the sequence itself is compared. The comparison of the sequences is case-independent. The logical union is an OR operation by default. Other available operations are: AND, XOR and NOT.

Algorithm

All the input sequences are kept in memory while the logical unions of the two input sets of sequences is calculated. listor is therefore restricted by the available memory.

Usage

Here is a sample session with listor

Write the logical OR of two lists:

% listor ../data/file2
Write a list file of the logical OR of two sets of sequences
List of USAs output file [file1.list]:

Command line arguments

Write a list file of the logical OR of two sets of sequences
Version: EMBOSS:6.5.0.0
Standard (Mandatory) qualifiers:
[-firstsequences] seqset Sequence set filename and optional format,
or reference (input USA)
[-secondsequences] seqset Sequence set filename and optional format,
or reference (input USA)
[-outfile] outfile [*.listor] The list of sequence names will
be written to this list file
Additional (Optional) qualifiers:
-operator menu [OR] The following logical operators combine
the sequences in the following ways:
OR - gives all that occur in one set or the
other
AND - gives only those which occur in both
sets
XOR - gives those which only occur in one
set or the other, but not in both
NOT - gives those which occur in the first
set except for those that also occur in the
second (Values: OR (OR - merger of both
sets); AND (AND - only those in both sets);
XOR (XOR - only those not in both sets); NOT
(NOT - those of the first set that are not
in the second))
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-firstsequences" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-scircular1 boolean Sequence is circular
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-secondsequences" associated qualifiers
-sbegin2 integer Start of each sequence to be used
-send2 integer End of each sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-scircular2 boolean Sequence is circular
-sformat2 string Input sequence format
-iquery2 string Input query fields or ID list
-ioffset2 integer Input start position offset
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
"-outfile" associated qualifiers
-odirectory3 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit

Qualifier

Type

Description

Allowed values

Default

Standard (Mandatory) qualifiers

[-firstsequences](Parameter 1)

seqset

Sequence set filename and optional format, or reference (input USA)

Readable set of sequences

Required

[-secondsequences](Parameter 2)

seqset

Sequence set filename and optional format, or reference (input USA)

Readable set of sequences

Required

[-outfile](Parameter 3)

outfile

The list of sequence names will be written to this list file

Output file

<*>.listor

Additional (Optional) qualifiers

-operator

list

The following logical operators combine the sequences in the following ways:
OR - gives all that occur in one set or the other
AND - gives only those which occur in both sets
XOR - gives those which only occur in one set or the other, but not in both
NOT - gives those which occur in the first set except for those that also occur in the second

OR

(OR - merger of both sets)

AND

(AND - only those in both sets)

XOR

(XOR - only those not in both sets)

NOT

(NOT - those of the first set that are not in the second)

OR

Advanced (Unprompted) qualifiers

(none)

Associated qualifiers

"-firstsequences" associated seqset qualifiers

-sbegin1-sbegin_firstsequences

integer

Start of each sequence to be used

Any integer value

0

-send1-send_firstsequences

integer

End of each sequence to be used

Any integer value

0

-sreverse1-sreverse_firstsequences

boolean

Reverse (if DNA)

Boolean value Yes/No

N

-sask1-sask_firstsequences

boolean

Ask for begin/end/reverse

Boolean value Yes/No

N

-snucleotide1-snucleotide_firstsequences

boolean

Sequence is nucleotide

Boolean value Yes/No

N

-sprotein1-sprotein_firstsequences

boolean

Sequence is protein

Boolean value Yes/No

N

-slower1-slower_firstsequences

boolean

Make lower case

Boolean value Yes/No

N

-supper1-supper_firstsequences

boolean

Make upper case

Boolean value Yes/No

N

-scircular1-scircular_firstsequences

boolean

Sequence is circular

Boolean value Yes/No

N

-sformat1-sformat_firstsequences

string

Input sequence format

Any string

-iquery1-iquery_firstsequences

string

Input query fields or ID list

Any string

-ioffset1-ioffset_firstsequences

integer

Input start position offset

Any integer value

0

-sdbname1-sdbname_firstsequences

string

Database name

Any string

-sid1-sid_firstsequences

string

Entryname

Any string

-ufo1-ufo_firstsequences

string

UFO features

Any string

-fformat1-fformat_firstsequences

string

Features format

Any string

-fopenfile1-fopenfile_firstsequences

string

Features file name

Any string

"-secondsequences" associated seqset qualifiers

-sbegin2-sbegin_secondsequences

integer

Start of each sequence to be used

Any integer value

0

-send2-send_secondsequences

integer

End of each sequence to be used

Any integer value

0

-sreverse2-sreverse_secondsequences

boolean

Reverse (if DNA)

Boolean value Yes/No

N

-sask2-sask_secondsequences

boolean

Ask for begin/end/reverse

Boolean value Yes/No

N

-snucleotide2-snucleotide_secondsequences

boolean

Sequence is nucleotide

Boolean value Yes/No

N

-sprotein2-sprotein_secondsequences

boolean

Sequence is protein

Boolean value Yes/No

N

-slower2-slower_secondsequences

boolean

Make lower case

Boolean value Yes/No

N

-supper2-supper_secondsequences

boolean

Make upper case

Boolean value Yes/No

N

-scircular2-scircular_secondsequences

boolean

Sequence is circular

Boolean value Yes/No

N

-sformat2-sformat_secondsequences

string

Input sequence format

Any string

-iquery2-iquery_secondsequences

string

Input query fields or ID list

Any string

-ioffset2-ioffset_secondsequences

integer

Input start position offset

Any integer value

0

-sdbname2-sdbname_secondsequences

string

Database name

Any string

-sid2-sid_secondsequences

string

Entryname

Any string

-ufo2-ufo_secondsequences

string

UFO features

Any string

-fformat2-fformat_secondsequences

string

Features format

Any string

-fopenfile2-fopenfile_secondsequences

string

Features file name

Any string

"-outfile" associated outfile qualifiers

-odirectory3-odirectory_outfile

string

Output directory

Any string

General qualifiers

-auto

boolean

Turn off prompts

Boolean value Yes/No

N

-stdout

boolean

Write first file to standard output

Boolean value Yes/No

N

-filter

boolean

Read first file from standard input, write first file to standard output

Boolean value Yes/No

N

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

N

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

N

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

Y

-help

boolean

Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose

Boolean value Yes/No

N

-warning

boolean

Report warnings

Boolean value Yes/No

Y

-error

boolean

Report errors

Boolean value Yes/No

Y

-fatal

boolean

Report fatal errors

Boolean value Yes/No

Y

-die

boolean

Report dying program messages

Boolean value Yes/No

Y

-version

boolean

Report version number and exit

Boolean value Yes/No

N

Input file format

The input sets of sequences can be of any valid USAs. The program was
written to perform logical operations on list files, but in practice,
wildcarded database entries and file names are also perfectly legal
specifications of the input sequences.

File: file1

File: file2

Output file format

The output is simply a list of the USAs (format and sequence
specification) resulting from the required logical union of the two sets
of input sequence.

The order that the USAs are written out is not necessarily the same as
the order of either of the input sets of sequences.

The results of the four types of logical union follows. Note that the
duplicated sequences in these two files have been given the same name.
This is not necessary for the operation of listor as it compares
the sequences themselves, not the ID names of the sequences.

Output files for usage example 3

File: file1.list

Output files for usage example 4

File: file1.list

Data files

None.

Notes

The inputs can be any valid USA but typically reference a list file. Some other reference such as a wildcarded database entries or file name are equally valid.

The (default) logical OR of the two sets of sequences is simply the result of merging the two sets of sequences. A sequences appearing in both input sets is referenced once only in the output file. A logical AND simply lists those sequences that occur in both sets of sequences.

A logical XOR lists those sequences that ONLY occur in the first set or only occur in the second set - sequences occuring in both sets are omitted (the opposite of an AND).

A logical NOT lists all those sequences in the first set except for those that also occur in the second set.

References

None.

Warnings

listor is restricted by the available memory. Doing logical unions involving all of the sequences in large databases, such as EMBL, is probably impractical unless you are lucky enough to have extraordinary amounts of memory on your machine.